In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants.
Identifieur interne : 000383 ( Main/Exploration ); précédent : 000382; suivant : 000384In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants.
Auteurs : Haruna I. Umar [Nigeria] ; Sunday S. Josiah [Nigeria] ; Tolulope P. Saliu [Nigeria] ; Tajudeen O. Jimoh [Thaïlande] ; Adeola Ajayi [Nigeria] ; Jamilu B. Danjuma [Nigeria]Source :
- Journal of Taibah University Medical Sciences [ 1658-3612 ] ; 2021.
Abstract
Objectives
Over the years,
Methods
The crystal structure of Mpro was retrieved from the Protein Data Bank, while the plant bioactive compounds were retrieved from Pubchem. Drug-likeness of the selected compounds and a control drug (hydroxychloroquine) were assessed, and the compounds that satisfied the drug-likeness rule were docked against Mpro. The docked complexes were analyzed using LigPlot and the protein-ligand profiler server. The top five compound hits were subjected to ADMET screening using the ADMETSar server.
Results
A total of 17 out of 22 screened compounds passed Lipinski's assessment. Additionally, the most active compounds from the investigated plants exhibited relative inhibitory potentials against Mpro compared with hydroxychloroquine, which alludes to their possible involvement in inhibiting the SARS-CoV-2 main protease replication process.
Conclusions
In our study, most of the active phytocomponents of the investigated plants exhibited relative inhibitory potentials against Mpro of SARS-CoV-2 and preferred pharmacological features when compared with hydroxychloroquine. These findings indicate these compounds are potentially antiviral candidates against SARS-CoV-2.
DOI: 10.1016/j.jtumed.2020.12.005
PubMed: 33437230
PubMed Central: PMC7787523
Affiliations:
Links toward previous steps (curation, corpus...)
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Josiah</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Saliu, Tolulope P" sort="Saliu, Tolulope P" uniqKey="Saliu T" first="Tolulope P" last="Saliu">Tolulope P. Saliu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Jimoh, Tajudeen O" sort="Jimoh, Tajudeen O" uniqKey="Jimoh T" first="Tajudeen O" last="Jimoh">Tajudeen O. Jimoh</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok</wicri:regionArea><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Ajayi, Adeola" sort="Ajayi, Adeola" uniqKey="Ajayi A" first="Adeola" last="Ajayi">Adeola Ajayi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Danjuma, Jamilu B" sort="Danjuma, Jamilu B" uniqKey="Danjuma J" first="Jamilu B" last="Danjuma">Jamilu B. Danjuma</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, Federal University, Birnin Kebbi, Kebbi State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Federal University, Birnin Kebbi, Kebbi State</wicri:regionArea><wicri:noRegion>Kebbi State</wicri:noRegion></affiliation></author></titleStmt><publicationStmt><idno type="wicri:source">PubMed</idno><date when="2021">2021</date><idno type="RBID">pubmed:33437230</idno><idno type="pmid">33437230</idno><idno type="doi">10.1016/j.jtumed.2020.12.005</idno><idno type="pmc">PMC7787523</idno><idno type="wicri:Area/Main/Corpus">000499</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Corpus" wicri:corpus="PubMed">000499</idno><idno type="wicri:Area/Main/Curation">000499</idno><idno type="wicri:explorRef" wicri:stream="Main" wicri:step="Curation">000499</idno><idno type="wicri:Area/Main/Exploration">000499</idno></publicationStmt><sourceDesc><biblStruct><analytic><title xml:lang="en">In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants.</title><author><name sortKey="Umar, Haruna I" sort="Umar, Haruna I" uniqKey="Umar H" first="Haruna I" last="Umar">Haruna I. Umar</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Josiah, Sunday S" sort="Josiah, Sunday S" uniqKey="Josiah S" first="Sunday S" last="Josiah">Sunday S. Josiah</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Saliu, Tolulope P" sort="Saliu, Tolulope P" uniqKey="Saliu T" first="Tolulope P" last="Saliu">Tolulope P. Saliu</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Jimoh, Tajudeen O" sort="Jimoh, Tajudeen O" uniqKey="Jimoh T" first="Tajudeen O" last="Jimoh">Tajudeen O. Jimoh</name><affiliation wicri:level="1"><nlm:affiliation>Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand.</nlm:affiliation><country xml:lang="fr">Thaïlande</country><wicri:regionArea>Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok</wicri:regionArea><wicri:noRegion>Bangkok</wicri:noRegion></affiliation></author><author><name sortKey="Ajayi, Adeola" sort="Ajayi, Adeola" uniqKey="Ajayi A" first="Adeola" last="Ajayi">Adeola Ajayi</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry, Federal University of Technology, Akure, Ondo State</wicri:regionArea><wicri:noRegion>Ondo State</wicri:noRegion></affiliation></author><author><name sortKey="Danjuma, Jamilu B" sort="Danjuma, Jamilu B" uniqKey="Danjuma J" first="Jamilu B" last="Danjuma">Jamilu B. Danjuma</name><affiliation wicri:level="1"><nlm:affiliation>Department of Biochemistry and Molecular Biology, Federal University, Birnin Kebbi, Kebbi State, Nigeria.</nlm:affiliation><country xml:lang="fr">Nigeria</country><wicri:regionArea>Department of Biochemistry and Molecular Biology, Federal University, Birnin Kebbi, Kebbi State</wicri:regionArea><wicri:noRegion>Kebbi State</wicri:noRegion></affiliation></author></analytic><series><title level="j">Journal of Taibah University Medical Sciences</title><idno type="eISSN">1658-3612</idno><imprint><date when="2021" type="published">2021</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en"><p><b>Objectives</b></p><p>Over the years, </p></div><div type="abstract" xml:lang="en"><p><b>Methods</b></p><p>The crystal structure of Mpro was retrieved from the Protein Data Bank, while the plant bioactive compounds were retrieved from Pubchem. Drug-likeness of the selected compounds and a control drug (hydroxychloroquine) were assessed, and the compounds that satisfied the drug-likeness rule were docked against Mpro. The docked complexes were analyzed using LigPlot and the protein-ligand profiler server. The top five compound hits were subjected to ADMET screening using the ADMETSar server.</p></div><div type="abstract" xml:lang="en"><p><b>Results</b></p><p>A total of 17 out of 22 screened compounds passed Lipinski's assessment. Additionally, the most active compounds from the investigated plants exhibited relative inhibitory potentials against Mpro compared with hydroxychloroquine, which alludes to their possible involvement in inhibiting the SARS-CoV-2 main protease replication process.</p></div><div type="abstract" xml:lang="en"><p><b>Conclusions</b></p><p>In our study, most of the active phytocomponents of the investigated plants exhibited relative inhibitory potentials against Mpro of SARS-CoV-2 and preferred pharmacological features when compared with hydroxychloroquine. These findings indicate these compounds are potentially antiviral candidates against SARS-CoV-2.</p></div></front></TEI><pubmed><MedlineCitation Status="PubMed-not-MEDLINE" Owner="NLM"><PMID Version="1">33437230</PMID><DateRevised><Year>2021</Year><Month>04</Month><Day>01</Day></DateRevised><Article PubModel="Print-Electronic"><Journal><ISSN IssnType="Electronic">1658-3612</ISSN><JournalIssue CitedMedium="Internet"><Volume>16</Volume><Issue>2</Issue><PubDate><Year>2021</Year><Month>Apr</Month></PubDate></JournalIssue><Title>Journal of Taibah University Medical Sciences</Title><ISOAbbreviation>J Taibah Univ Med Sci</ISOAbbreviation></Journal><ArticleTitle>In-silico analysis of the inhibition of the SARS-CoV-2 main protease by some active compounds from selected African plants.</ArticleTitle><Pagination><MedlinePgn>162-176</MedlinePgn></Pagination><ELocationID EIdType="doi" ValidYN="Y">10.1016/j.jtumed.2020.12.005</ELocationID><Abstract><AbstractText Label="Objectives" NlmCategory="UNASSIGNED">Over the years, <i>Azadirachta indica, Mangifera indica,</i> and <i>Moringa oleifera</i> have been shown to possess some antiviral characteristics. This study applies molecular docking techniques to assess inhibitory effects of some bioactive compounds from the plants mentioned above against the main protease (Mpro), a key protein involved in SARS-CoV-2 replication. Furthermore, adsorption, distribution, metabolism, excretion, and toxicity (ADMET) profiles for screened compounds were predicted <i>in silico</i>.</AbstractText><AbstractText Label="Methods" NlmCategory="UNASSIGNED">The crystal structure of Mpro was retrieved from the Protein Data Bank, while the plant bioactive compounds were retrieved from Pubchem. Drug-likeness of the selected compounds and a control drug (hydroxychloroquine) were assessed, and the compounds that satisfied the drug-likeness rule were docked against Mpro. The docked complexes were analyzed using LigPlot and the protein-ligand profiler server. The top five compound hits were subjected to ADMET screening using the ADMETSar server.</AbstractText><AbstractText Label="Results" NlmCategory="UNASSIGNED">A total of 17 out of 22 screened compounds passed Lipinski's assessment. Additionally, the most active compounds from the investigated plants exhibited relative inhibitory potentials against Mpro compared with hydroxychloroquine, which alludes to their possible involvement in inhibiting the SARS-CoV-2 main protease replication process.</AbstractText><AbstractText Label="Conclusions" NlmCategory="UNASSIGNED">In our study, most of the active phytocomponents of the investigated plants exhibited relative inhibitory potentials against Mpro of SARS-CoV-2 and preferred pharmacological features when compared with hydroxychloroquine. These findings indicate these compounds are potentially antiviral candidates against SARS-CoV-2.</AbstractText><CopyrightInformation>© 2020 The Authors.</CopyrightInformation></Abstract><AuthorList CompleteYN="Y"><Author ValidYN="Y"><LastName>Umar</LastName><ForeName>Haruna I</ForeName><Initials>HI</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Josiah</LastName><ForeName>Sunday S</ForeName><Initials>SS</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Saliu</LastName><ForeName>Tolulope P</ForeName><Initials>TP</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Jimoh</LastName><ForeName>Tajudeen O</ForeName><Initials>TO</Initials><AffiliationInfo><Affiliation>Faculty of Pharmaceutical Sciences, Department of Pharmacognosy and Pharmaceutical Botany, Chulalongkorn University, Bangkok, Thailand.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Ajayi</LastName><ForeName>Adeola</ForeName><Initials>A</Initials><AffiliationInfo><Affiliation>Department of Biochemistry, Federal University of Technology, Akure, Ondo State, Nigeria.</Affiliation></AffiliationInfo></Author><Author ValidYN="Y"><LastName>Danjuma</LastName><ForeName>Jamilu B</ForeName><Initials>JB</Initials><AffiliationInfo><Affiliation>Department of Biochemistry and Molecular Biology, Federal University, Birnin Kebbi, Kebbi State, Nigeria.</Affiliation></AffiliationInfo></Author></AuthorList><Language>eng</Language><PublicationTypeList><PublicationType UI="D016428">Journal Article</PublicationType></PublicationTypeList><ArticleDate DateType="Electronic"><Year>2021</Year><Month>01</Month><Day>06</Day></ArticleDate></Article><MedlineJournalInfo><Country>Saudi Arabia</Country><MedlineTA>J Taibah Univ Med Sci</MedlineTA><NlmUniqueID>101621911</NlmUniqueID><ISSNLinking>1658-3612</ISSNLinking></MedlineJournalInfo><OtherAbstract Type="Publisher" Language="ara"><AbstractText Label="أهداف البحث" NlmCategory="UNASSIGNED">على مر السنين، أثبتت أزاديراشتا إنديكا، مانجيفيرا إنديكا ومورينجا أوليفيرا أن لديهم بعض الخصائص المضادة للفيروسات. تطبق هذه الدراسة تقنيات الالتحام الجزيئي لتقييم الآثار المثبطة لبعض المركبات البيولوجية النشطة من النباتات المذكورة أعلاه ضد الإنزيم البروتيني الرئيس، وهو البروتين الرئيس المتضمن في تكاثر فيروس سارس-كوفيد-٢. وعلاوة على ذلك، تم توقع فحص المركبات للكشف عن الامتزاز والتوزيع والتمثيل الغذائي والإفراز والسمية في السيليكو.</AbstractText><AbstractText Label="طرق البحث" NlmCategory="UNASSIGNED">تم الحصول على التركيب البلوري للإنزيم البروتيني الرئيس من قاعدة بيانات البروتين، بينما تم الحصول على المركبات البيولوجية النشطة من الكيمياء المنشورة. وتم تقييم تشابه الأدوية للمركبات المختارة ودواء التحكم (الهيدروكسيكلوروكوين). كما تمت ترسية المركبات المطابقة لقاعدة الأدوية المشابهة ضد الإنزيم البروتيني الرئيس، وتم تحليل المجمع الرأسي باستخدام خدمة التعريف ليج بلوت والبروتين المجند. تعرضت أفضل خمس مركبات ناجحة إلى فحص الامتزاز والتوزيع والتمثيل الغذائي والإفراز والسمية باستخدام معرف سار ادمت.</AbstractText><AbstractText Label="النتائج" NlmCategory="UNASSIGNED">١٧ من ٢٢ من المركبات التي تم فحصها اجتازت تقييم ليبينسكي. بالإضافة إلى ذلك، أظهرت أكثر المركبات نشاطا من النباتات التي تم فحصها إمكانات مثبطة نسبيا ضد الإنزيم البروتيني الرئيس عند مقارنتها بالهيدروكسيكلوروكوين، الأمر الذي يلمح إلى مشاركتهم المحتملة في تثبيط عملية التكاثر للإنزيم البروتيني الرئيس لفيروس سارس-كوفيد-٢.</AbstractText><AbstractText Label="الاستنتاجات" NlmCategory="UNASSIGNED">في هذه الدراسة، معظم المكونات النباتية النشطة عرضت إمكانات مثبطة ضد الإنزيم البروتيني الرئيس لفيروس سارس-كوفيد-٢ والخصائص الدوائية المفضلة عند مقارنتها بالهيدروكسيكلوروكوين، مما يجعلها مضادات محتملة للفيروسات ضد مرض فيروس كورونا.</AbstractText></OtherAbstract><KeywordList Owner="NOTNLM"><Keyword MajorTopicYN="N">Azadirachta indica</Keyword><Keyword MajorTopicYN="N">Mangifera indica</Keyword><Keyword MajorTopicYN="N">Moringa oleifera</Keyword><Keyword MajorTopicYN="N">SARS-CoV-2 main protease</Keyword><Keyword MajorTopicYN="N">in silico</Keyword></KeywordList></MedlineCitation><PubmedData><History><PubMedPubDate PubStatus="received"><Year>2020</Year><Month>09</Month><Day>18</Day></PubMedPubDate><PubMedPubDate PubStatus="revised"><Year>2020</Year><Month>11</Month><Day>28</Day></PubMedPubDate><PubMedPubDate PubStatus="accepted"><Year>2020</Year><Month>12</Month><Day>13</Day></PubMedPubDate><PubMedPubDate PubStatus="pubmed"><Year>2021</Year><Month>1</Month><Day>14</Day><Hour>6</Hour><Minute>0</Minute></PubMedPubDate><PubMedPubDate PubStatus="medline"><Year>2021</Year><Month>1</Month><Day>14</Day><Hour>6</Hour><Minute>1</Minute></PubMedPubDate><PubMedPubDate PubStatus="entrez"><Year>2021</Year><Month>1</Month><Day>13</Day><Hour>6</Hour><Minute>11</Minute></PubMedPubDate></History><PublicationStatus>ppublish</PublicationStatus><ArticleIdList><ArticleId IdType="pubmed">33437230</ArticleId><ArticleId IdType="doi">10.1016/j.jtumed.2020.12.005</ArticleId><ArticleId IdType="pii">S1658-3612(20)30206-7</ArticleId><ArticleId IdType="pmc">PMC7787523</ArticleId></ArticleIdList><pmc-dir>pmcsd</pmc-dir>
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